Seuquencing services

Tools and services for MMCI sequencing pipeline

• URL: sequencing.int.mou.cz

BBM Sequencing info

• Allows Biobanker to find if a set of samples does also have sequencing data
• Biobanker uploades a CSV or Excel file with specified format, the service adds new column with information of sequencing data are present for a given column

Pathology data retrieval

• Allows pathologists to get back their uploded data from SensitiveCloud.
• They can use predictive number to find a relevant sequencing run and then copy the run into seq server /seq/NO_BACKUP_SPACE/RETRIEVED

Running the service

1. Go to seq server into /services
2. Run docker compose

docker-compose -f compose.prod.yml up -d

3. Initialize database

docker-compose exec web python manage.py create_db

4. Populate database with existing data

docker-compose exec web python manage.py fill_db

5. (Optional) Verify if the data were sucesfully uploaded into the database

docker-compose exec db psql --username=<prod_username> --dbname=<prod_db_name>